What is the spike protein of the corona and why is it feared that the mutation will be resistant to vaccines

The emergence of a new version of the corona virus has sparked renewed interest in a part of the virus known as the spike protein. A virology expert explains what the spike protein is and what the effect of changes in it is on vaccines

By: Conor Bamford, Research Fellow, Virology, Queen's University Belfast

Note: The article was published on THE CONVERSATIONS website before the South African variant was discovered, but as far as is known, what was said is also relevant to it.

The emergence of a new version of the corona virus has sparked renewed interest in a part of the virus known as the spike protein.

The new variant carries a number of strange changes in the spike protein compared to other variants - its relatives and this is one of the reasons why it is more worrying than other, harmless changes in the virus we have seen in the past. The new mutations may change the biochemistry of the spike and affect how the virus infects.

The spike protein is also the basis of the current COVID-19 vaccines, which seek to generate an immune response against it. But what exactly is spike protein (or spike protein) and why is it so important?

Diagram showing the structure of the SARS-CoV-2 corona virus molecule in full and in parts

invade cells

In the world of parasites, many bacterial or fungal pathogens can survive on their own without a host cell and infect. But viruses cannot. Instead, they have to get inside cells to replicate themselves, where they use the cell's own biochemical machinery to build new virus particles and spread them to other cells or other people.

Our cells have evolved to repel such intrusions. One of the main defenses they have against invaders is their outer coating or shell. The envelope consisting of a fatty layer that protects the enzymes, proteins and DNA inside a cell. Due to the biochemical nature of lipids, the outer surface is charged with a very negative and repulsive charge. Viruses must cross this barrier to gain access to the cell.

Like the living cell, the corona virus itself is surrounded by a fatty membrane known as an envelope. In order to gain entry to the interior of the cell, enveloped viruses use proteins (or glycoproteins because they are often covered in slippery sugar molecules) to fuse their membrane with that of the cells and take over the cell.

The spike protein of the corona viruses is such a viral glycoprotein. The Ebola virus also has a thin envelope. The flu virus has two while the herpes viruses have five.

The architecture of the thorns

The spike protein consists of a linear chain of 1,273 amino acids, neatly folded into a structure, in which up to 23 sugar molecules are embedded. Spike proteins like to stick together and three separate spike molecules bind together to form a functional unit.

The spike can be divided into separate functional units called domains, which fulfill different biochemical functions of the protein, such as attaching to the target cell, rubbing with the membrane, and those that allow the spikes to "sit" on the viral envelope.

The spike protein of SARS-CoV-2 surrounds a roughly spherical viral particle embedded within the envelope and protrudes ready to latch onto innocent cells. It is estimated that there are about 26 spikes per virus.

One of these functional units binds to a protein on the surface of our cells called ACE2, which activates the uptake of the virus particle and ultimately causes the membranes to fuse. The sharp increase in spike activity is also involved in other processes such as assembly, structural stability and evasion from the immune system.

Immunization against the changes in the spike protein

Given that the spike is an essential protein for virus function, many antiviral vaccines and drugs target viral glycoproteins.

For SARS-CoV-2, the vaccines produced by Pfizer and Biotech, as well as by Moderna, instruct our immune system to produce our own version of the spike protein shortly after vaccination. After the production of the spike protein inside our cells, the immune system begins to work, starting with the production of antibodies and T cells/

An electron microscope image shows four SARS-CoV-2 virus particles.

One of the most concerning features of the SARS-CoV-2 spike protein is how it changes over time during the evolution of the virus. The protein encoded within the viral genome can change and consequently also change its biochemical properties.

Most of the mutations will not be beneficial for the virus and will not prevent the spike protein from functioning but some of them may cause changes and create the new version of the virus that will have a selective advantage by making it more infectious.

One way this can happen is through a mutation in a part of a spike protein that prevents the immune system's antibodies from acting against it. Another way would be to make the spikes more "sticky" for our cells.

That's why new mutations that change the way the spike functions are particularly worrisome - they may affect how we control the spread of SARS-CoV-2. The new variants found in the UK and elsewhere contain mutations on the surface of the spike and in parts of the protein involved in entering cells.

Now it is necessary to do experiments to find out if - and how these mutations significantly change the increase in morbidity, and if our current control measures (vaccines) remain effective.

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• For an article in The Conversation